Harvard:Biophysics 101/2007/Notebook:Michael Wang/2007-2-13

I've managed to figure out how to get clustal working (or at least executing on a windows machine). These steps are from Shawn. I've just pasted them here for convenience. Code will follow shortly.

From the desktop, right click My Computer and click properties.
In the System Properties window, click on the Advanced tab.
In the Advanced section, click the Environment Variables button.
Finally, in the Environment Variables window, highlight the path variable
in the Systems Variable section and click edit. Add or modify the path
lines with the paths you wish the computer to access. Each different
directory is separated with a semicolon as shown below.

C:\Program Files;C:\Winnt;C:\Winnt\System32

Add the directory containing clustalw to your path.

In other words, if you unzipped the clustalw zip file into C:\Documents and Settings\Mike\Desktop\clustalw,
your final path variable should look like:

C:\Program Files;C:\Winnt;C:\Winnt\System32; C:\Documents and Settings\Mike\Desktop\clustalw

In your actual program, you can call clustalw with the following code (also from Shawn)

#!/usr/bin/env python

import os
from Bio import Clustalw

cline = Clustalw.MultipleAlignCL(os.path.join(os.curdir, 'apoe.fasta'))
cline.set_output('test.aln')
alignment = Clustalw.do_alignment(cline)

I hope this helps